Search Results for "linux tool" - Page 2
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Showing 65 open source projects for "linux tool"
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW....
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting... -
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CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices... -
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ADTEx
Aberration detection in tumour exome
Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. -
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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Pugsly PubChem Client
Command-line, PubChem PUG client, written in Python
Client to the PubChem Tool (PCT), The Power User Gateway (PUG). Written in Python and developed for use with Linux. -
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Pathomx
Workflow-based data analysis built on IPython
Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. -
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IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
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EducationalLCS
eLCS - Educational Learning Classifier System
Educational Learning Classifier System (eLCS) is a set of learning classifier system (LCS) educational demos designed to introduce students or researchers to the basics of a modern Michigan-style LCS algorithm. This eLCS package includes 5 different implementations of a basic LCS algorithm, as part of a 6 stage set of demos that will be paired with the first introductory LCS textbook. Each eLCS implementations (from demo 2 up to demo 6) progressively add major components of the entire... -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are... -
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DeDAY
MLE survival analysis: Gompertz, Weibull, Logistic and mixed morality.
DeDAY (Demography Data Analyses) is a tool of analyzing demography data. It supports Gompertz, Weibull and Logistic distributions. DeDay also supports mixed mortality models based on these distribution such as the Gompertz-Makeham distribution. Distributions such as Gompertz describes only age-dependent mortality, which increases over time. Mixed mortality models, such as in Gompertz-Makeham distribution, consider a more general case where mortality is consist of both age-dependent and... -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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pyBioImage
Biological Imaging Software suite
The pyBioImage is a python a python based biological imaging suite tailored to the problem of finding Germinal Center "spots" within multidimensional microscopy images as it is described in the research paper: "Software tool for 3D extraction of germinal centers", by David N. Olivieri, Merly Escalona and Jose Faro. -
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The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
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AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data.
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NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
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NumericalFISH is a bioinformatics graphical tool for easy analysis of BLAST or BLAT results, especially aimed at the study of duplications or segmental duplications.
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H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
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ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
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Volumetric file viewer for the human brain. Easy, powerful and flexible fMRI/MRI brain research and clinical neuro-surgery tool. Using state of the art open VTK 3D library, the proven Qt GUI toolkit, coded in Python.
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FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra
